MolNFT v1 · #157841 · protein
HLA-A2 (A*02:01) bound to a peptide from the epstein-barr virus BRLF1 protein
6NCA · Replication and transcription activator: “HLA-A2 (A*02:01) bound to a peptide from the epstein-barr virus BRLF1 protein”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #157841 on GenesisL1: 3D structure, binding…
- PDB
- 6NCA
- Type
- protein
- Length
- 7,680 residues
- Chains
- 60
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication and transcription activator; HLA class I histocompatibility antigen, a-2…
- UniProt
- Q3KSS7, P01892, P61769
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, u, z, y, 8, w, 4, 3, W, 6, x, 5, X, v, 2, U, Z, V, 7, 1 | Replication and transcription activator | protein | 9 | 0% helix, 0% strand | Q3KSS7 |
| A, B, C, D, E, F, G, H, S, J, K, L, M, N, O, P, Q, R, I, T | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 26% helix, 40% strand | P01892 |
| a, b, c, d, f, g, h, s, j, k, l, m, n, o, p, q, r, i, t, e | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.77 | 0.96 | 19 | empty |
| 2 | 1039 | 0.75 | 0.78 | 93 | empty |
| 3 | 1097 | 0.74 | 0.77 | 96 | empty |
| 4 | 1054 | 0.74 | 0.77 | 98 | empty |
| 5 | 145 | 0.74 | 0.92 | 24 | empty |
Interfaces
98 interfaces between chains.
- A–a · 1492 Ų buried · 15 hydrogen bonds · protein-protein
- E–e · 1474 Ų buried · 19 hydrogen bonds · protein-protein
- P–p · 1467 Ų buried · 21 hydrogen bonds · protein-protein
- K–k · 1466 Ų buried · 17 hydrogen bonds · protein-protein
- G–g · 1458 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide (disulfide).
Compared structures
- 6NCA · HLA-A2 (A*02:01) bound to a peptide from the Epstein-Barr virus BRLF1 protein · the same entry in another collection · chain w against w, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q3KSS7
- Every structure of UniProt P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6NCA · PDBe 6NCA · UniProt Q3KSS7 · UniProt P01892 · UniProt P61769
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