5V2C
RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, T (A, a) | Photosystem II protein D1 | polymer | 344 | 38235.6 | 2 | UniProt (P51765) | Thermosynechococcus vulcanus | PSII D1 protein,Photosystem II Q(B) protein |
| 2 | B, U (B, b) | Photosystem II CP47 reaction center protein | polymer | 506 | 56141.7 | 2 | UniProt (D0VWR1) | Thermosynechococcus vulcanus | PSII 47 kDa protein,Protein CP-47 |
| 3 | C, V (C, c) | Photosystem II CP43 reaction center protein | polymer | 458 | 49940.0 | 2 | UniProt (D0VWR7) | Thermosynechococcus vulcanus | PSII 43 kDa protein,Protein CP-43 |
| 4 | D, W (D, d) | Photosystem II D2 protein | polymer | 342 | 38418.0 | 2 | UniProt (D0VWR8) | Thermosynechococcus vulcanus | PSII D2 protein,Photosystem Q(A) protein |
| 5 | E, X (E, e) | Cytochrome b559 subunit alpha | polymer | 83 | 9449.6 | 2 | UniProt (P12238) | Thermosynechococcus vulcanus | PSII reaction center subunit V |
| 6 | F, Y (F, f) | Cytochrome b559 subunit beta | polymer | 44 | 4936.7 | 2 | UniProt (P12239) | Thermosynechococcus vulcanus | PSII reaction center subunit VI |
| 7 | G, Z (H, h) | Photosystem II reaction center protein H | polymer | 65 | 7227.6 | 2 | UniProt (P19052) | Thermosynechococcus vulcanus | PSII-H |
| 8 | AA, H (I, i) | Photosystem II reaction center protein I | polymer | 38 | 4438.3 | 2 | UniProt (P12240) | Thermosynechococcus vulcanus | PSII-I,PSII 4.4 kDa protein |
| 9 | BA, I (J, j) | Photosystem II reaction center protein J | polymer | 40 | 4103.8 | 2 | UniProt (Q7DGD4) | Thermosynechococcus vulcanus | PSII-J |
| 10 | CA, J (K, k) | Photosystem II reaction center protein K | polymer | 37 | 4101.9 | 2 | UniProt (P19054) | Thermosynechococcus vulcanus | PSII-K |
| 11 | DA, K (L, l) | Photosystem II reaction center protein L | polymer | 37 | 4299.0 | 2 | UniProt (P12241) | Thermosynechococcus vulcanus | PSII-L |
| 12 | EA, L (M, m) | Photosystem II reaction center protein M | polymer | 36 | 4009.7 | 2 | UniProt (P12312) | Thermosynechococcus vulcanus | PSII-M |
| 13 | FA, M (O, o) | Photosystem II manganese-stabilizing polypeptide | polymer | 245 | 26665.7 | 2 | UniProt (D0VWR2) | Thermosynechococcus vulcanus | MSP |
| 14 | GA, N (T, t) | Photosystem II reaction center protein T | polymer | 32 | 3906.7 | 2 | UniProt (P12313) | Thermosynechococcus vulcanus | PSII-Tc |
| 15 | HA, O (U, u) | Photosystem II 12 kDa extrinsic protein | polymer | 104 | 11656.0 | 2 | UniProt (P56152) | Thermosynechococcus vulcanus | PS II complex 12 kDa extrinsic protein,PSII-U |
| 16 | IA, P (V, v) | Cytochrome c-550 | polymer | 137 | 15148.3 | 2 | UniProt (P0A387) | Thermosynechococcus vulcanus | Cytochrome c550,Low-potential cytochrome c |
| 17 | JA, Q (Y, y) | Photosystem II reaction center protein Ycf12 | polymer | 30 | 3228.0 | 2 | UniProt (D0VWR3) | Thermosynechococcus vulcanus | |
| 18 | KA, R (X, x) | Photosystem II reaction center protein X | polymer | 41 | 4322.2 | 2 | UniProt (D0VWR4) | Thermosynechococcus vulcanus | |
| 19 | LA, S (Z, z) | Photosystem II reaction center protein Z | polymer | 62 | 6766.2 | 2 | UniProt (D0VWR5) | Thermosynechococcus vulcanus | PSII-Z |
| 20 | MA, PJ (A, a) | CA-MN4-O5 CLUSTER | non-polymer | 339.8 | 2 | Chemie (OEX) | PROTEIN CP-47 | ||
| 21 | NA, QJ (A, a) | FE (II) ION | non-polymer | 55.8 | 2 | Chemie (FE2) PubChem (27284) | |||
| 22 | DR, OA, PA, RI, RJ... (v, A, V, a) | CHLORIDE ION | non-polymer | 35.5 | 6 | Chemie (CL) PubChem (312) | |||
| 23 | JQ, QA, TJ (m, A, a) | BICARBONATE ION | non-polymer | 61.0 | 3 | Chemie (BCT) PubChem (769) | |||
| 24 | AC, AE, AL, BC, BE... (B, C, b, d, D...) | CHLOROPHYLL A | non-polymer | 893.5 | 70 | Chemie (CLA) | |||
| 25 | AO, HF, TA, WJ (d, D, A, a) | PHEOPHYTIN A | non-polymer | 871.2 | 4 | Chemie (PHO) | |||
| 26 | CC, CQ, DC, EC, EE... (B, k, C, b, d...) | BETA-CAROTENE | non-polymer | 536.9 | 22 | Chemie (BCR) PubChem (573) PubChem (21672398) PubChem (176490061) PubChem (177696266) PubChem (46783370) PubChem (46846294) PubChem (54603957) PubChem (54612003) PubChem (86765360) PubChem (5315709) PubChem (5280489) PubChem (91827292) PubChem (92863345) PubChem (5353436) PubChem (5356616) PubChem (5927371) PubChem (124919640) PubChem (92863346) PubChem (92863347) PubChem (92863348) PubChem (6477957) PubChem (100990628) PubChem (101525094) PubChem (101525095) PubChem (9828626) PubChem (10256668) PubChem (12305639) PubChem (12305640) PubChem (12305642) PubChem (12305644) PubChem (12305647) PubChem (12305652) PubChem (146673260) PubChem (152743364) PubChem (124919639) PubChem (160505766) PubChem (129651951) PubChem (132274419) PubChem (145925599) PubChem (159562859) PubChem (172654026) PubChem (172878405) PubChem (173398668) | |||
| 27 | GO, NF, WA, ZJ (d, D, A, a) | 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE | non-polymer | 749.2 | 4 | Chemie (PL9) PubChem (23304240) PubChem (20286) PubChem (21881166) PubChem (5375177) PubChem (6323474) PubChem (6325820) PubChem (6433402) | |||
| 28 | AK, BB, EK, EQ, HB... (a, A, l, h, x...) | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL | non-polymer | 795.1 | 11 | Chemie (SQD) PubChem (25147486) PubChem (25235342) PubChem (42607399) PubChem (159321) PubChem (481096) PubChem (5459390) PubChem (102201395) PubChem (134765349) PubChem (9810997) PubChem (9918745) PubChem (10219110) PubChem (10373133) PubChem (14463145) | |||
| 29 | BK, CN, DN, FC, HL... (a, c, B, b, C...) | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE | non-polymer | 787.2 | 14 | Chemie (LMG) | |||
| 30 | AB, AP, AR, BI, BO... (A, f, u, O, d...) | GLYCEROL | non-polymer | 92.1 | 60 | Chemie (GOL) PubChem (753) | |||
| 31 | CB, CR, DH, EN, GC... (A, u, I, c, B...) | DODECYL-BETA-D-MALTOSIDE | non-polymer | 510.6 | 18 | Chemie (LMT) | |||
| 32 | AG, DB, DQ, GK, IO... (E, A, l, a, d...) | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE | non-polymer | 723.0 | 12 | Chemie (LHG) PubChem (46936292) PubChem (446440) PubChem (73416066) PubChem (65144) PubChem (9547104) PubChem (13305396) PubChem (11846227) PubChem (138986743) | |||
| 33 | AD, AF, AJ, BD, BF... (B, C, V, E, A...) | TETRAETHYLENE GLYCOL | non-polymer | 194.2 | 57 | Chemie (PG4) PubChem (8200) | |||
| 34 | AH, AM, BH, BM, CD... (H, b, B, f, C...) | TRIETHYLENE GLYCOL | non-polymer | 150.2 | 65 | Chemie (PGE) | |||
| 35 | AQ, FF, IB, IH, IM... (j, C, A, I, b...) | HEXAETHYLENE GLYCOL | non-polymer | 282.3 | 17 | Chemie (P6G) PubChem (17472) | |||
| 36 | CH, GF, HJ, II, JH... (H, C, V, O, I...) | 1,2-ETHANEDIOL | non-polymer | 62.1 | 22 | Chemie (EDO) | |||
| 37 | EP, HN, LB, LQ, NK... (h, c, B, o, b...) | CALCIUM ION | non-polymer | 40.1 | 6 | Chemie (CA) PubChem (271) | |||
| 38 | AI, DP, FK, FN, GN... (O, h, a, c, B...) | heptyl 1-thio-beta-D-glucopyranoside | non-polymer | 294.4 | 24 | Chemie (HTG) PubChem (17754029) PubChem (22844385) PubChem (71317209) PubChem (561567) PubChem (656917) PubChem (135074) PubChem (95858610) PubChem (96361182) PubChem (96361183) PubChem (97041763) PubChem (101138253) PubChem (10979306) PubChem (11335391) PubChem (11392262) | |||
| 39 | BQ, GJ, LD, MD, OR... (j, V, B, x, L...) | PENTAETHYLENE GLYCOL | non-polymer | 238.3 | 7 | Chemie (1PE) PubChem (62551) | |||
| 40 | AN, BN, GE, GP, HE... (c, C, h, d, D...) | DIGALACTOSYL DIACYL GLYCEROL (DGDG) | non-polymer | 949.3 | 10 | Chemie (DGD) PubChem (24865462) PubChem (24865463) PubChem (50904896) PubChem (53480668) PubChem (46936671) PubChem (448441) PubChem (447899) PubChem (4629344) PubChem (15991538) PubChem (154573294) PubChem (171123158) PubChem (134746152) PubChem (140529801) | |||
| 41 | MG, XO (E, e) | PROTOPORPHYRIN IX CONTAINING FE | non-polymer | 616.5 | 2 | Chemie (HEM) | |||
| 42 | LH, PG, WP, ZO (J, F, j, f) | MAGNESIUM ION | non-polymer | 24.3 | 4 | Chemie (MG) PubChem (888) | |||
| 43 | ER, SI (v, V) | HEME C | non-polymer | 618.5 | 2 | Chemie (HEC) | |||
| 44 | FJ (V) | NONAETHYLENE GLYCOL | non-polymer | 414.5 | 1 | Chemie (2PE) PubChem (4867) | |||
| 45 | TP (i) | 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL | non-polymer | 370.4 | 1 | Chemie (PE8) PubChem (78798) | |||
| 46 | AS, AT, BS, BT, CS... (L, x, M, z, O...) | water | water | 18.0 | 3787 | Chemie (HOH) |
Sequence modifications
A, a: 1 - 344 (UniProt: P51765)
B, b: 2 - 505 (UniProt: D0VWR1)
C, c: 23 - 473 (UniProt: D0VWR7)
J, j: 1 - 40 (UniProt: Q7DGD4)
K, k: 10 - 46 (UniProt: P19054)
M, m: 1 - 36 (UniProt: P12312)
O, o: 4 - 246 (UniProt: D0VWR2)
X, x: 2 - 41 (UniProt: D0VWR4)
| PDB | External Database | Details |
|---|---|---|
| Pro 279 | Arg 279 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ser 506 | - | expression tag |
| Asp 507 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Glu 16 | - | expression tag |
| Ala 17 | - | expression tag |
| Ala 18 | - | expression tag |
| Asn 19 | - | expression tag |
| Ser 20 | - | expression tag |
| Ile 21 | - | expression tag |
| Phe 22 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Glu 2 | Met 2 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Leu 33 | Phe 24 | conflict |
| Trp 39 | Val 30 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Leu 8 | Phe 8 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ala 2 | - | expression tag |
| Ala 3 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Met 1 | - | initiating methionine |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 38 |
| Total formula weight | 593990.2 | |
| Non-Polymers* | Number of molecules | 446 |
| Total formula weight | 173999.6 | |
| All* | Total formula weight | 767989.8 |
