4P5M
Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C, E, G (A, C, E, G) | HLA class II histocompatibility antigen, DP alpha 1 chain | polymer | 183 | 21169.6 | 4 | UniProt (P20036) Pfam (PF00993) Pfam (PF07654) | Homo sapiens (Human) | DP(W3),DP(W4),HLA-SB alpha chain,MHC class II DP3-alpha,MHC class II DPA1 |
| 2 | B, D, F, H (B, D, F, H) | peptide,HLA class II histocompatibility antigen, DP beta 1 chain | polymer | 212 | 24341.1 | 4 | UniProt (Q5EP54) Pfam (PF00969) Pfam (PF07654) UniProt (by SIFTS) (P04440) | Homo sapiens (Human) | HLA class II histocompatibility antigen,DP(W2) beta chain,MHC class II antigen DPB1 |
| 3 | I, K, N (I, K, N) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 3 | In PDB GlyTouCan (G42666HT) | |||
| 4 | J (J) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 830.8 | 1 | In PDB GlyTouCan (G57331KL) | |||
| 5 | L (L) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 627.6 | 1 | In PDB GlyTouCan (G26744ZJ) | |||
| 6 | M (M) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 789.7 | 1 | In PDB GlyTouCan (G59760RN) | |||
| 7 | O (O) | beta-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 1 | In PDB GlyTouCan (G29706YY) | |||
| 8 | P, Q (A, C) | SODIUM ION | non-polymer | 23.0 | 2 | Chemie (NA) | |||
| 9 | R (E) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 1 | Chemie (NAG) | |||
| 10 | S, T, U, V, W... (A, B, C, D, E...) | water | water | 18.0 | 1660 | Chemie (HOH) |
Sequence modifications
B, D, F, H: -25 - -14 (PDB: 4P5M)
B, D, F, H: 3 - 189 (UniProt: Q5EP54)
| PDB | External Database | Details |
|---|---|---|
| Gly -13 | - | linker |
| Gly -12 | - | linker |
| Ser -11 | - | linker |
| Leu -10 | - | linker |
| Val -9 | - | linker |
| Pro -8 | - | linker |
| Arg -7 | - | linker |
| Gly -6 | - | linker |
| Ser -5 | - | linker |
| Gly -4 | - | linker |
| Gly -3 | - | linker |
| Gly -2 | - | linker |
| Gly -1 | - | linker |
| PDB | External Database | Details |
|---|---|---|
| Ser 3 | Thr 32 | variant |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 8 |
| Total formula weight | 182042.6 | |
| Branched | Number of molecules | 7 |
| Total formula weight | 4107.9 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 267.2 | |
| All* | Total formula weight | 186417.7 |
