3LEL
Structural Insight into the Sequence-Dependence of Nucleosome Positioning
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005694 | cellular_component | chromosome |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0000786 | cellular_component | nucleosome |
| D | 0003677 | molecular_function | DNA binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005694 | cellular_component | chromosome |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005694 | cellular_component | chromosome |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005634 | cellular_component | nucleus |
| F | 0005694 | cellular_component | chromosome |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0000786 | cellular_component | nucleosome |
| H | 0003677 | molecular_function | DNA binding |
| H | 0005515 | molecular_function | protein binding |
| H | 0005634 | cellular_component | nucleus |
| H | 0005694 | cellular_component | chromosome |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| K | 0000786 | cellular_component | nucleosome |
| K | 0003677 | molecular_function | DNA binding |
| K | 0005515 | molecular_function | protein binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0005654 | cellular_component | nucleoplasm |
| K | 0005694 | cellular_component | chromosome |
| K | 0030527 | molecular_function | structural constituent of chromatin |
| K | 0046982 | molecular_function | protein heterodimerization activity |
| L | 0000786 | cellular_component | nucleosome |
| L | 0003677 | molecular_function | DNA binding |
| L | 0005515 | molecular_function | protein binding |
| L | 0005634 | cellular_component | nucleus |
| L | 0005694 | cellular_component | chromosome |
| L | 0030527 | molecular_function | structural constituent of chromatin |
| L | 0046982 | molecular_function | protein heterodimerization activity |
| M | 0000786 | cellular_component | nucleosome |
| M | 0003677 | molecular_function | DNA binding |
| M | 0005634 | cellular_component | nucleus |
| M | 0005694 | cellular_component | chromosome |
| M | 0030527 | molecular_function | structural constituent of chromatin |
| M | 0046982 | molecular_function | protein heterodimerization activity |
| N | 0000786 | cellular_component | nucleosome |
| N | 0003677 | molecular_function | DNA binding |
| N | 0005515 | molecular_function | protein binding |
| N | 0005634 | cellular_component | nucleus |
| N | 0005694 | cellular_component | chromosome |
| N | 0030527 | molecular_function | structural constituent of chromatin |
| N | 0046982 | molecular_function | protein heterodimerization activity |
| O | 0000786 | cellular_component | nucleosome |
| O | 0003677 | molecular_function | DNA binding |
| O | 0005515 | molecular_function | protein binding |
| O | 0005634 | cellular_component | nucleus |
| O | 0005654 | cellular_component | nucleoplasm |
| O | 0005694 | cellular_component | chromosome |
| O | 0030527 | molecular_function | structural constituent of chromatin |
| O | 0046982 | molecular_function | protein heterodimerization activity |
| P | 0000786 | cellular_component | nucleosome |
| P | 0003677 | molecular_function | DNA binding |
| P | 0005515 | molecular_function | protein binding |
| P | 0005634 | cellular_component | nucleus |
| P | 0005694 | cellular_component | chromosome |
| P | 0030527 | molecular_function | structural constituent of chromatin |
| P | 0046982 | molecular_function | protein heterodimerization activity |
| Q | 0000786 | cellular_component | nucleosome |
| Q | 0003677 | molecular_function | DNA binding |
| Q | 0005634 | cellular_component | nucleus |
| Q | 0005694 | cellular_component | chromosome |
| Q | 0030527 | molecular_function | structural constituent of chromatin |
| Q | 0046982 | molecular_function | protein heterodimerization activity |
| R | 0000786 | cellular_component | nucleosome |
| R | 0003677 | molecular_function | DNA binding |
| R | 0005515 | molecular_function | protein binding |
| R | 0005634 | cellular_component | nucleus |
| R | 0005694 | cellular_component | chromosome |
| R | 0030527 | molecular_function | structural constituent of chromatin |
| R | 0046982 | molecular_function | protein heterodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN N 3132 |
| Chain | Residue |
| N | GLU102 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN O 3152 |
| Chain | Residue |
| D | VAL45 |
| O | ASP77 |
| site_id | AC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN T 3134 |
| Chain | Residue |
| T | DG61 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 3135 |
| Chain | Residue |
| J | DG27 |
| S | DT67 |
| site_id | AC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 3136 |
| Chain | Residue |
| I | DG27 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 3137 |
| Chain | Residue |
| J | DG61 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 3138 |
| Chain | Residue |
| J | DG48 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN T 3139 |
| Chain | Residue |
| T | DG64 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN G 3140 |
| Chain | Residue |
| G | GLU91 |
| site_id | BC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 3142 |
| Chain | Residue |
| I | DG61 |
| site_id | BC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN T 3143 |
| Chain | Residue |
| T | DG27 |
| site_id | BC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 3144 |
| Chain | Residue |
| I | DG-2 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN T 3145 |
| Chain | Residue |
| T | DT67 |
| T | DA68 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN S 3146 |
| Chain | Residue |
| S | DG64 |
| S | DG65 |
| site_id | BC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN T 3147 |
| Chain | Residue |
| T | DA-3 |
| T | DG-2 |
| site_id | BC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 3148 |
| Chain | Residue |
| J | DG64 |
| site_id | BC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 3149 |
| Chain | Residue |
| J | DG-2 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 3150 |
| Chain | Residue |
| I | DG-35 |
| I | DG-34 |
| site_id | CC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN S 3151 |
| Chain | Residue |
| S | DG-2 |
| site_id | CC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN S 3153 |
| Chain | Residue |
| S | DG61 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN T 3154 |
| Chain | Residue |
| T | DG-56 |
| T | DA-57 |
| site_id | CC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN S 3155 |
| Chain | Residue |
| S | DT47 |
| S | DG48 |
| site_id | CC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN T 3156 |
| Chain | Residue |
| T | DG-34 |
| T | DG-35 |
| site_id | CC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN S 3157 |
| Chain | Residue |
| S | DA26 |
| S | DG27 |
| site_id | CC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN S 3158 |
| Chain | Residue |
| S | DG-35 |
| S | DG-34 |
| site_id | CC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN T 3159 |
| Chain | Residue |
| T | DG48 |
| T | DG49 |
| site_id | CC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN I 3160 |
| Chain | Residue |
| I | DT63 |
| I | DG64 |
| I | DG65 |
| site_id | DC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 3161 |
| Chain | Residue |
| I | DG48 |
| site_id | DC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN T 3162 |
| Chain | Residue |
| T | DT5 |
| site_id | DC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN J 3164 |
| Chain | Residue |
| J | DG64 |
| J | DG65 |
| J | DA66 |
| site_id | DC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 3165 |
| Chain | Residue |
| J | DT5 |
| site_id | DC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 3166 |
| Chain | Residue |
| I | DT4 |
| J | DA-3 |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| B | GLY14-HIS18 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG89-GLY111 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 16 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P0C1H4 |
| Chain | Residue | Details |
| D | LYS2 | |
| N | LYS9 | |
| N | LYS12 | |
| N | LYS17 | |
| R | LYS2 | |
| R | LYS9 | |
| R | LYS12 | |
| R | LYS17 | |
| D | LYS9 | |
| D | LYS12 | |
| D | LYS17 | |
| H | LYS2 | |
| H | LYS9 | |
| H | LYS12 | |
| H | LYS17 | |
| N | LYS2 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:12757711 |
| Chain | Residue | Details |
| D | SER11 | |
| H | SER11 | |
| N | SER11 | |
| R | SER11 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
| Chain | Residue | Details |
| D | SER109 | |
| H | SER109 | |
| N | SER109 | |
| R | SER109 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0C1H4 |
| Chain | Residue | Details |
| D | LYS117 | |
| F | LYS5 | |
| H | LYS117 | |
| P | LYS5 | |
| N | LYS117 | |
| R | LYS117 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 16 |
| Details | MOD_RES: N6-propionyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS8 | |
| L | LYS16 | |
| L | LYS44 | |
| L | LYS79 | |
| P | LYS8 | |
| P | LYS16 | |
| P | LYS44 | |
| P | LYS79 | |
| B | LYS16 | |
| B | LYS44 | |
| B | LYS79 | |
| F | LYS8 | |
| F | LYS16 | |
| F | LYS44 | |
| F | LYS79 | |
| L | LYS8 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS12 | |
| B | LYS20 | |
| F | LYS12 | |
| F | LYS20 | |
| L | LYS12 | |
| L | LYS20 | |
| P | LYS12 | |
| P | LYS20 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS31 | |
| B | LYS91 | |
| F | LYS31 | |
| F | LYS91 | |
| L | LYS31 | |
| L | LYS91 | |
| P | LYS31 | |
| P | LYS91 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine; by PAK2 => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | SER47 | |
| F | SER47 | |
| L | SER47 | |
| P | SER47 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | TYR51 | |
| B | TYR88 | |
| F | TYR51 | |
| F | TYR88 | |
| L | TYR51 | |
| L | TYR88 | |
| P | TYR51 | |
| P | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS59 | |
| E | LYS64 | |
| K | LYS18 | |
| K | LYS23 | |
| K | LYS27 | |
| K | LYS36 | |
| K | LYS64 | |
| O | LYS18 | |
| O | LYS23 | |
| O | LYS27 | |
| O | LYS36 | |
| F | LYS59 | |
| O | LYS64 | |
| L | LYS59 | |
| P | LYS59 | |
| A | LYS64 | |
| E | LYS18 | |
| E | LYS23 | |
| E | LYS27 | |
| E | LYS36 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS77 | |
| F | LYS77 | |
| L | LYS77 | |
| P | LYS77 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS31 | |
| F | LYS31 | |
| L | LYS31 | |
| P | LYS31 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| A | LYS37 | |
| B | LYS91 | |
| K | LYS37 | |
| F | LYS91 | |
| L | LYS91 | |
| P | LYS91 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | TYR41 | |
| E | TYR41 | |
| K | TYR41 | |
| O | TYR41 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| A | LYS56 | |
| A | LYS79 | |
| E | LYS56 | |
| E | LYS79 | |
| K | LYS56 | |
| K | LYS79 | |
| O | LYS56 | |
| O | LYS79 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | SER57 | |
| E | SER57 | |
| K | SER57 | |
| O | SER57 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | THR80 | |
| A | THR107 | |
| E | THR80 | |
| E | THR107 | |
| K | THR80 | |
| K | THR107 | |
| O | THR80 | |
| O | THR107 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER86 | |
| E | SER86 | |
| K | SER86 | |
| O | SER86 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS115 | |
| E | LYS115 | |
| K | LYS115 | |
| O | LYS115 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS122 | |
| E | LYS122 | |
| K | LYS122 | |
| O | LYS122 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 4 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | CYS110 | |
| E | CYS110 | |
| K | CYS110 | |
| O | CYS110 |
