2KODA

A high-resolution nmr structure of the dimeric c-terminal domain of hiv-1 ca
Total Genus 21
Loading diagram...

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
21
sequence length
88
structure length
88
Chain Sequence
MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL
Loading diagram...

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

molecule tags Viral protein
molecule keywords HIV-1 CA C-terminal domain
publication title Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
pubmed doi rcsb
source organism Hiv-1 m:b_hxb2r
total genus 21
structure length 88
sequence length 88
chains with identical sequence B
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2009-09-18
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A 2kodA00
3H47A 2JO0A 4M0IA 4WYMA 2JYGA 1E6JP 2ONTA 2XXMA 3LRYA 3VRLC 2M8LA 1A8OA 3P05A 1EOQA 4U0CA 5JPAA 4XFXA 3MGEA 5HGNA 4COPA 3G29A 2BUOA 2M8NA 2EIAA 3DPHA 3G21A 4IPYA 1QRJA 3DS0A 2M8PA 4XROA 2LF4A 3DS1A 3DS5A 1BAJA 3DTJA 4XFYA 3H4EA 4QNBA 3G1IA 4XRQA 4U0BA 3DS3A 3DS2A 1EIAA 3NTEA 1A43A 2L6EA 5HGMA 5HGOA 4U0DA 3G1GA 4XFZA 4U0AA 1D1DA 4COCA 2JYLA 2XV6A 3DS4A 4U0FA 2KODA 2XT1A 4U0EA 3G28A 3G26A 4PH1A 4PH0A 3G0VA 5DCKA 5I4TG 1AUMA 5HGLA
chains in the Genus database with same CATH superfamily
1E0HA 1VQ6P 2JO0A 1EMVA 1M74A 1EOQA 3CXCO 2VSQA 3EJBA 3DTJA 1BXIA 4QNBA 2PEIA 2QEXP 3I56P 4UHPB 2AFDA 2KWLA 1VQ9P 2KGEA 1VKUA 3H47A 1YJNP 3U43A 3E2DA 2LKIA 1VQOP 2FQ2A 4COPA 3CCSP 1M90Q 2QNWA 1ZMBA 3DS5A 2M5RA 3GKLC 5KP7B 2AVAA 4DG9A 2VLNA 1QVFO 2XT1A 1KLPA 1K73Q 2CGQA 3VRLC 5KP6B 2Z46A 3G4SP 2FQ1A 2DNWA 3DPHA 4BPGA 7CEIA 1S72P 3G1IA 3CCVP 1VQPP 2K92A 4U0EA 2N6YA 2KG6A 3RG6C 2KG9A 3HZQA 3Q20A 2GZGA 1VQLP 4H2XC 2EHSA 1YJ9P 2MY5A 1VQMP 2K5XA 3G21A 5HGOA 3OW2O 4CA3A 2N5IA 1K9MQ 2ROQA 4PXHB 1VQ5P 1NJIQ 2LMLA 5KP8B 1KD1Q 2FHSC 2XXMA 2GZEA 4R0MA 2K0YA 3P05A 3CMEP 2JU1A 3GJNA 3CCJP 2M8NA 1F80D 2GYKA 1K30A 2CQ8A 3DS1A 1BAJA 1UNKA 2MVVA 2KOOA 1D1DA 2OTLP 3DS4A 2KODA 2FVAA 2GZIA 5EJDA 1W2BO 2LPKA 5JPAA 2GDXA 3MGEA 2K0DX 2KOPA 4BPHA 2LIUA 1DNYA 2VLOA 3EJDA 4IZ6A 4U0BA 5BS2A 1EIAA 2QA4P 1IUQA 2MD9A 1L0HA 2JYLA 2XV6A 4F37A 2PY8A 2MVUA 5CZDB 2LTEA 1ZNVA 3M1MA 1ACPA 2KG8A 2K93A 3H4EA 2OARA 4HKGA 2LOLA 2L22A 2CNRA 1IMQA 4QKOA 4WYMA 2JYGA 2EHTA 1VQ4P 3G29A 2JQ4A 2MR8A 4H2YC 4GR6A 3G6EP 4BPFA 3H0DA 1M6EX 1MZ8A 5F2NA 4U0AA 2PENA 1FR2A 2FQ0A 4PH1A 2CG5B 1AUMA 2VLPA 5HGLA 1K8AQ 2LL8A 3B4QA 2JU2A 2M8LA 2KR5A 1RO0A 2XZ0D 1UJZA 2GDWA 3G71P 2L0QA 2KOSA 1VQKP 1JJ2O 4U0DA 3B5IA 2OTJP 1Q81Q 2NO8A 3G28A 2PEOA 5HV8A 1E6JP 1RO2A 1DV5A 2MF4A 2EIAA 3CCLP 4XROA 2FADA 3LMOA 1Q82Q 1RNIA 2JB0A 5F2OA 3NTEA 5HGMA 1VQ7P 3G1GA 2JBGA 2PNGA 1N8RQ 5EW5E 2FACA 1GXHA 3CC2P 5BS1A 3NY7B 1VQNP 2KGAA 2X2BA 4XFYA 1GPJA 2CWOA 1T8KA 2K0XA 4H2WC 4MRTC 3G0VA 3CCRP 1KQSO 1HQBA 2EG5A 1Z6MA 2PEJA 3CE7A 3CCEP 1Q7YQ 1GXGA 1IMPA 3WBHA 4IPYA 1QVGO 2M8PA 2WPTA 2KGCA 3I55P 4PWVB 3GZMA 2K2QA 2PEQA 2GZJA 2KW2A 5HVCA 4PH0A 2VLQA 1VHNA 3RG2A 2BUOA 2BHVA 3CPWO 2L4BA 2JAZA 2FVEA 2Z45A 1AF8A 2P9XA 2AF8A 1HY8A 3G26A 3CC7P 1VQ8P 2GZFA 1YIJP 1Q86Q 2PEKA 2Z44A 2FVFA 1QRJA 2FAEA 3CCUP 3CD6P 3DS3A 2L6EA 2GDYA 3CC4P 2MR7A 2XZ1C 2ERHA 2JGPA 2AFEA 5I4TG 1YI2P 2K94A 2KOQA 2N6ZA 4U0CA 2LIWA 3CMAP 1YITP 2N98A 1M1KQ 2LF4A 1X3OA 2N5HA 3EJEA 4NEOA 4XRQA 1KC8Q 2L9FA 5F2KA 4COCA 4U0FA 2KORA 1NQ4A 5DCKA 1M6NA 2N50A 3CCMP 4M0IA 2ONTA 3LRYA 1A8OA 4XFXA 2KGDA 1YHQP 5HGNA 3GZLA 3DS0A 1YJWP 2DGYA 3CCQP 3DS2A 1A43A 1OR5A 4XFZA 4GR2A 1L0IA 1CEIA 3HYBA 1AYIA 2E1MA 2EFJA 2PEMA
chains in the Genus database with same CATH topology
1VQ6P 2JO0A 1NJIQ 1KD1Q 2XXMA 2M8LA 3P05A 1M74A 1EOQA 3CXCO 1RO0A 3CMEP 3CCJP 3G71P 2BUOA 2M8NA 2BHVA 3CPWO 1K30A 3DS1A 1BAJA 3DTJA 4QNBA 1VQKP 2Z45A 1JJ2O 2PEIA 4U0DA 2QEXP 2P9XA 3I56P 3B5IA 1D1DA 2OTJP 2OTLP 1Q81Q 3DS4A 2KODA 3G28A 3G26A 2PEOA 1VQ9P 3CC7P 3H47A 1YJNP 1VQ8P 1E6JP 1YIJP 1W2BO 1Q86Q 2PEKA 3E2DA 2Z44A 5JPAA 1RO2A 1VQOP 3MGEA 4COPA 2EIAA 3CCLP 3CCSP 1QRJA 1M90Q 1ZMBA 4XROA 3DS5A 3CCUP 1Q82Q 1RNIA 3CD6P 5BS2A 4U0BA 3DS3A 1EIAA 3NTEA 5F2OA 5HGMA 2L6EA 2QA4P 1VQ7P 3G1GA 1IUQA 3CC4P 1QVFO 2JYLA 2XV6A 2XT1A 1N8RQ 1K73Q 5I4TG 1YI2P 2PY8A 3VRLC 3CC2P 1K8AQ 4U0CA 2Z46A 5BS1A 3G4SP 3CMAP 1VQNP 3DPHA 1YITP 3M1MA 1M1KQ 2LF4A 1S72P 4XFYA 3H4EA 4XRQA 3G1IA 3CCVP 2OARA 5HGLA 1KC8Q 5F2KA 4COCA 2CWOA 1VQPP 4U0FA 4U0EA 3G0VA 5DCKA 3RG6C 3HZQA 3CCRP 1M6NA 1KQSO 3Q20A 1VQLP 4WYMA 4M0IA 3CCMP 2EG5A 2JYGA 2PEJA 2ONTA 3LRYA 1YJ9P 3CCEP 1A8OA 1Q7YQ 4XFXA 1YHQP 1VQMP 1VQ4P 5HGNA 3G29A 3WBHA 4IPYA 3G21A 3DS0A 1QVGO 2M8PA 1YJWP 2DGYA 4GR6A 3I55P 3G6EP 3H0DA 3CCQP 2PEQA 1VQ5P 3DS2A 1A43A 5HGOA 1M6EX 4XFZA 3OW2O 5F2NA 4GR2A 4U0AA 2PENA 1K9MQ 4PH0A 4PH1A 3HYBA 2E1MA 1AUMA 2EFJA 2PEMA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3H47 A;  2JO0 A;  4M0I A;  4WYM A;  2JYG A;  1E6J P;  2ONT A;  2XXM A;  3LRY A;  3VRL C;  2M8L A;  1A8O A;  3P05 A;  1EOQ A;  4U0C A;  5JPA A;  4XFX A;  3MGE A;  5HGN A;  4COP A;  3G29 A;  2BUO A;  2M8N A;  2EIA A;  3DPH A;  3G21 A;  4IPY A;  1QRJ A;  3DS0 A;  2M8P A;  4XRO A;  2LF4 A;  3DS1 A;  3DS5 A;  1BAJ A;  3DTJ A;  4XFY A;  3H4E A;  4QNB A;  3G1I A;  4XRQ A;  4U0B A;  3DS3 A;  3DS2 A;  1EIA A;  3NTE A;  1A43 A;  2L6E A;  5HGM A;  5HGO A;  4U0D A;  3G1G A;  4XFZ A;  4U0A A;  1D1D A;  4COC A;  2JYL A;  2XV6 A;  3DS4 A;  4U0F A;  2KOD A;  2XT1 A;  4U0E A;  3G28 A;  3G26 A;  4PH1 A;  4PH0 A;  3G0V A;  5DCK A;  5I4T G;  1AUM A;  5HGL A; 
#chains in the Genus database with same CATH topology
 1E0H A;  1VQ6 P;  2JO0 A;  1EMV A;  1M74 A;  1EOQ A;  3CXC O;  2VSQ A;  3EJB A;  3DTJ A;  1BXI A;  4QNB A;  2PEI A;  2QEX P;  3I56 P;  4UHP B;  2AFD A;  2KWL A;  1VQ9 P;  2KGE A;  1VKU A;  3H47 A;  1YJN P;  3U43 A;  3E2D A;  2LKI A;  1VQO P;  2FQ2 A;  4COP A;  3CCS P;  1M90 Q;  2QNW A;  1ZMB A;  3DS5 A;  2M5R A;  3GKL C;  5KP7 B;  2AVA A;  4DG9 A;  2VLN A;  1QVF O;  2XT1 A;  1KLP A;  1K73 Q;  2CGQ A;  3VRL C;  5KP6 B;  2Z46 A;  3G4S P;  2FQ1 A;  2DNW A;  3DPH A;  4BPG A;  7CEI A;  1S72 P;  3G1I A;  3CCV P;  1VQP P;  2K92 A;  4U0E A;  2N6Y A;  2KG6 A;  3RG6 C;  2KG9 A;  3HZQ A;  3Q20 A;  2GZG A;  1VQL P;  4H2X C;  2EHS A;  1YJ9 P;  2MY5 A;  1VQM P;  2K5X A;  3G21 A;  5HGO A;  3OW2 O;  4CA3 A;  2N5I A;  1K9M Q;  2ROQ A;  4PXH B;  1VQ5 P;  1NJI Q;  2LML A;  5KP8 B;  1KD1 Q;  2FHS C;  2XXM A;  2GZE A;  4R0M A;  2K0Y A;  3P05 A;  3CME P;  2JU1 A;  3GJN A;  3CCJ P;  2M8N A;  1F80 D;  2GYK A;  1K30 A;  2CQ8 A;  3DS1 A;  1BAJ A;  1UNK A;  2MVV A;  2KOO A;  1D1D A;  2OTL P;  3DS4 A;  2KOD A;  2FVA A;  2GZI A;  5EJD A;  1W2B O;  2LPK A;  5JPA A;  2GDX A;  3MGE A;  2K0D X;  2KOP A;  4BPH A;  2LIU A;  1DNY A;  2VLO A;  3EJD A;  4IZ6 A;  4U0B A;  5BS2 A;  1EIA A;  2QA4 P;  1IUQ A;  2MD9 A;  1L0H A;  2JYL A;  2XV6 A;  4F37 A;  2PY8 A;  2MVU A;  5CZD B;  2LTE A;  1ZNV A;  3M1M A;  1ACP A;  2KG8 A;  2K93 A;  3H4E A;  2OAR A;  4HKG A;  2LOL A;  2L22 A;  2CNR A;  1IMQ A;  4QKO A;  4WYM A;  2JYG A;  2EHT A;  1VQ4 P;  3G29 A;  2JQ4 A;  2MR8 A;  4H2Y C;  4GR6 A;  3G6E P;  4BPF A;  3H0D A;  1M6E X;  1MZ8 A;  5F2N A;  4U0A A;  2PEN A;  1FR2 A;  2FQ0 A;  4PH1 A;  2CG5 B;  1AUM A;  2VLP A;  5HGL A;  1K8A Q;  2LL8 A;  3B4Q A;  2JU2 A;  2M8L A;  2KR5 A;  1RO0 A;  2XZ0 D;  1UJZ A;  2GDW A;  3G71 P;  2L0Q A;  2KOS A;  1VQK P;  1JJ2 O;  4U0D A;  3B5I A;  2OTJ P;  1Q81 Q;  2NO8 A;  3G28 A;  2PEO A;  5HV8 A;  1E6J P;  1RO2 A;  1DV5 A;  2MF4 A;  2EIA A;  3CCL P;  4XRO A;  2FAD A;  3LMO A;  1Q82 Q;  1RNI A;  2JB0 A;  5F2O A;  3NTE A;  5HGM A;  1VQ7 P;  3G1G A;  2JBG A;  2PNG A;  1N8R Q;  5EW5 E;  2FAC A;  1GXH A;  3CC2 P;  5BS1 A;  3NY7 B;  1VQN P;  2KGA A;  2X2B A;  4XFY A;  1GPJ A;  2CWO A;  1T8K A;  2K0X A;  4H2W C;  4MRT C;  3G0V A;  3CCR P;  1KQS O;  1HQB A;  2EG5 A;  1Z6M A;  2PEJ A;  3CE7 A;  3CCE P;  1Q7Y Q;  1GXG A;  1IMP A;  3WBH A;  4IPY A;  1QVG O;  2M8P A;  2WPT A;  2KGC A;  3I55 P;  4PWV B;  3GZM A;  2K2Q A;  2PEQ A;  2GZJ A;  2KW2 A;  5HVC A;  4PH0 A;  2VLQ A;  1VHN A;  3RG2 A;  2BUO A;  2BHV A;  3CPW O;  2L4B A;  2JAZ A;  2FVE A;  2Z45 A;  1AF8 A;  2P9X A;  2AF8 A;  1HY8 A;  3G26 A;  3CC7 P;  1VQ8 P;  2GZF A;  1YIJ P;  1Q86 Q;  2PEK A;  2Z44 A;  2FVF A;  1QRJ A;  2FAE A;  3CCU P;  3CD6 P;  3DS3 A;  2L6E A;  2GDY A;  3CC4 P;  2MR7 A;  2XZ1 C;  2ERH A;  2JGP A;  2AFE A;  5I4T G;  1YI2 P;  2K94 A;  2KOQ A;  2N6Z A;  4U0C A;  2LIW A;  3CMA P;  1YIT P;  2N98 A;  1M1K Q;  2LF4 A;  1X3O A;  2N5H A;  3EJE A;  4NEO A;  4XRQ A;  1KC8 Q;  2L9F A;  5F2K A;  4COC A;  4U0F A;  2KOR A;  1NQ4 A;  5DCK A;  1M6N A;  2N50 A;  3CCM P;  4M0I A;  2ONT A;  3LRY A;  1A8O A;  4XFX A;  2KGD A;  1YHQ P;  5HGN A;  3GZL A;  3DS0 A;  1YJW P;  2DGY A;  3CCQ P;  3DS2 A;  1A43 A;  1OR5 A;  4XFZ A;  4GR2 A;  1L0I A;  1CEI A;  3HYB A;  1AYI A;  2E1M A;  2EFJ A;  2PEM A; 
#chains in the Genus database with same CATH homology
 1VQ6 P;  2JO0 A;  1NJI Q;  1KD1 Q;  2XXM A;  2M8L A;  3P05 A;  1M74 A;  1EOQ A;  3CXC O;  1RO0 A;  3CME P;  3CCJ P;  3G71 P;  2BUO A;  2M8N A;  2BHV A;  3CPW O;  1K30 A;  3DS1 A;  1BAJ A;  3DTJ A;  4QNB A;  1VQK P;  2Z45 A;  1JJ2 O;  2PEI A;  4U0D A;  2QEX P;  2P9X A;  3I56 P;  3B5I A;  1D1D A;  2OTJ P;  2OTL P;  1Q81 Q;  3DS4 A;  2KOD A;  3G28 A;  3G26 A;  2PEO A;  1VQ9 P;  3CC7 P;  3H47 A;  1YJN P;  1VQ8 P;  1E6J P;  1YIJ P;  1W2B O;  1Q86 Q;  2PEK A;  3E2D A;  2Z44 A;  5JPA A;  1RO2 A;  1VQO P;  3MGE A;  4COP A;  2EIA A;  3CCL P;  3CCS P;  1QRJ A;  1M90 Q;  1ZMB A;  4XRO A;  3DS5 A;  3CCU P;  1Q82 Q;  1RNI A;  3CD6 P;  5BS2 A;  4U0B A;  3DS3 A;  1EIA A;  3NTE A;  5F2O A;  5HGM A;  2L6E A;  2QA4 P;  1VQ7 P;  3G1G A;  1IUQ A;  3CC4 P;  1QVF O;  2JYL A;  2XV6 A;  2XT1 A;  1N8R Q;  1K73 Q;  5I4T G;  1YI2 P;  2PY8 A;  3VRL C;  3CC2 P;  1K8A Q;  4U0C A;  2Z46 A;  5BS1 A;  3G4S P;  3CMA P;  1VQN P;  3DPH A;  1YIT P;  3M1M A;  1M1K Q;  2LF4 A;  1S72 P;  4XFY A;  3H4E A;  4XRQ A;  3G1I A;  3CCV P;  2OAR A;  5HGL A;  1KC8 Q;  5F2K A;  4COC A;  2CWO A;  1VQP P;  4U0F A;  4U0E A;  3G0V A;  5DCK A;  3RG6 C;  3HZQ A;  3CCR P;  1M6N A;  1KQS O;  3Q20 A;  1VQL P;  4WYM A;  4M0I A;  3CCM P;  2EG5 A;  2JYG A;  2PEJ A;  2ONT A;  3LRY A;  1YJ9 P;  3CCE P;  1A8O A;  1Q7Y Q;  4XFX A;  1YHQ P;  1VQM P;  1VQ4 P;  5HGN A;  3G29 A;  3WBH A;  4IPY A;  3G21 A;  3DS0 A;  1QVG O;  2M8P A;  1YJW P;  2DGY A;  4GR6 A;  3I55 P;  3G6E P;  3H0D A;  3CCQ P;  2PEQ A;  1VQ5 P;  3DS2 A;  1A43 A;  5HGO A;  1M6E X;  4XFZ A;  3OW2 O;  5F2N A;  4GR2 A;  4U0A A;  2PEN A;  1K9M Q;  4PH0 A;  4PH1 A;  3HYB A;  2E1M A;  1AUM A;  2EFJ A;  2PEM A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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